Explore the vast range of titles available.

Selective autophagy of damaged mitochondria requires autophagy receptors optineurin (OPTN), NDP52 (CALCOCO2), TAX1BP1, and p62 (SQSTM1) linking ubiquitinated cargo to autophagic membranes. By using quantitative proteomics, we show that Tank-binding kinase 1 (TBK1) phosphorylates all four receptors on several autophagyrelevant sites, including the ubiquitin- and LC3-binding domains of OPTN and p62/SQSTM1 as well as the SKICH domains of NDP52 and TAX1BP1. Constitutive interaction of TBK1 with OPTN and the ability of OPTN to bind to ubiquitin chains are essential for TBK1 recruitment and kinase activation on mitochondria. TBK1 in turn phosphorylates OPTN’s UBAN domain at S473, thereby expanding the binding capacity of OPTN to diverse Ub chains. In combination with phosphorylation of S177 and S513, this posttranslational modification promotes recruitment and retention of OPTN/TBK1 on ubiquitinated, damaged mitochondria. Moreover, phosphorylation of OPTN on S473 enables binding to pS65 Ub chains and is also implicated in PINK1-driven and Parkin-independent mitophagy. Thus, TBK1-mediated phosphorylation of autophagy receptors creates a signal amplification loop operating in selective autophagy of damaged mitochondria.

Lysine acetylation is a posttranslational modification that is dynamically regulated by the activity of acetyltransferases and deacetylases. The human and mouse genomes encode 18 different lysine deacetylases (KDACs) which are key regulators of many cellular processes. Identifying substrates of KDACs and pinpointing the regulated acetylation sites on target proteins may provide important information about the molecular basis of their functions. Here we apply quantitative proteomics to identify endogenous substrates of the mitochondrial deacetylase Sirtuin 3 (Sirt3) by comparing site-specific acetylation in wild-type murine embryonic fibroblasts to Sirt3 knockout cells. We confirm Sirt3-regulated acetylation of several mitochondrial proteins in human cells by comparing acetylation in U2OS cells overexpressing Sirt3 to U2OS cells in which Sirt3 expression was reduced by shRNA. Our data demonstrate that ablation of Sirt3 significantly increases acetylation at dozens of sites on mitochondrial proteins. Substrates of Sirt3 are implicated in various metabolic pathways, including fatty acid metabolism and the tricarboxylic acid cycle. These results imply broader regulatory roles of Sirt3 in the mitochondria by modulating acetylation on diverse substrates. The experimental strategy described here is generic and can be applied to identify endogenous substrates of other lysine deacetylases.

Direct numerical simulations (DNS) of turbulent thermal convection in a box-shaped domain with regular surface roughness at the heated bottom and cooled top surfaces are conducted for Prandtl number $\\mathit{Pr}=0.786$ and Rayleigh numbers $\\mathit{Ra}$ between $10^{6}$ and $10^{8}$ . The surface roughness is introduced by four parallelepiped equidistantly distributed obstacles attached to the bottom plate, and four obstacles located symmetrically at the top plate. By varying $\\mathit{Ra}$ and the height and width of the obstacles, we investigate the influence of the regular wall roughness on the turbulent heat transport, measured by the Nusselt number $\\mathit{Nu}$ . For fixed $\\mathit{Ra}$ , the change in the value of $\\mathit{Nu}$ is determined not only by the covering area of the surface, i.e. the obstacle height, but also by the distance between the obstacles. The heat flux enhancement is found to be largest for wide cavities between the obstacles which can be ‘washed out’ by the flow. This is also manifested in an empirical relation, which is based on the DNS data. We further discuss theoretical limiting cases for very wide and very narrow obstacles and combine them into a simple model for the heat flux enhancement due to the wall roughness, without introducing any free parameters. This model predicts well the general trends and the order of magnitude of the heat flux enhancement obtained in the DNS. In the $\\mathit{Nu}$ versus $\\mathit{Ra}$ scaling, the obstacles work in two ways: for smaller $\\mathit{Ra}$ an increase of the scaling exponent compared to the smooth case is found, which is connected to the heat flux entering the cavities from below. For larger $\\mathit{Ra}$ the scaling exponent saturates to the one for smooth plates, which can be understood as a full washing-out of the cavities. The latter is also investigated by considering the strength of the mean secondary flow in the cavities and its relation to the wind (i.e. the large-scale circulation), that develops in the core part of the domain. Generally, an increase in the roughness height leads to stronger flows both in the cavities and in the bulk region, while an increase in the width of the obstacles strengthens only the large-scale circulation of the fluid and weakens the secondary flows. An increase of the Rayleigh number always leads to stronger flows, both in the cavities and in the bulk.

Acute myeloid leukemia (AML) is a heterogeneous malignancy characterized by the accumulation of undifferentiated white blood cells (blasts) in the bone marrow. Valosin-containing protein (VCP) is an abundant molecular chaperone that extracts ubiquitylated substrates from protein complexes and cellular compartments prior to their degradation by the proteasome. We found that treatment of AML cell lines with the VCP inhibitor CB-5083 leads to an accumulation of ubiquitylated proteins, activation of unfolded protein response (UPR) and apoptosis. Using quantitative mass spectrometry-based proteomics we assessed the effects of VCP inhibition on the cellular ubiquitin-modified proteome. We could further show that CB-5083 decreases the survival of the AML cell lines THP-1 and MV4-11 in a concentration-dependent manner, and acts synergistically with the antimetabolite cytarabine and the BH3-mimetic venetoclax. Finally, we showed that prolonged treatment of AML cells with CB-5083 leads to development of resistance mediated by mutations in VCP . Taken together, inhibition of VCP leads to a lethal unfolded protein response in AML cells and might be a relevant therapeutic strategy for treatment of AML, particularly when combined with other drugs. The toxicity and development of resistance possibly limit the utility of VCP inhibitors and have to be further explored in animal models and clinical trials.

Europe’s recent summer droughts have had devastating ecological and economic consequences, but the severity and cause of these extremes remain unclear. Here we present 27,080 annually resolved and absolutely dated measurements of tree-ring stable carbon and oxygen (δ 13 C and δ 18 O) isotopes from 21 living and 126 relict oaks ( Quercus spp.) used to reconstruct central European summer hydroclimate from 75  bce to 2018  ce . We find that the combined inverse δ 13 C and δ 18 O values correlate with the June–August Palmer Drought Severity Index from 1901–2018 at 0.73 ( P  < 0.001). Pluvials around 200, 720 and 1100  ce , and droughts around 40, 590, 950 and 1510  ce and in the twenty-first century, are superimposed on a multi-millennial drying trend. Our reconstruction demonstrates that the sequence of recent European summer droughts since 2015  ce is unprecedented in the past 2,110 years. This hydroclimatic anomaly is probably caused by anthropogenic warming and associated changes in the position of the summer jet stream. European summer droughts in recent years are anomalously severe compared with those of the previous 2,000 years, according to a synthesis of annually resolved tree-ring carbon and oxygen isotope records.

BRAF is a serine/threonine-specific protein kinase that regulates the MAPK/ERK signaling pathway, and mutations in the BRAF gene are considered oncogenic drivers in diverse types of cancer. Based on the signaling mechanism, oncogenic BRAF mutations can be assigned to three different classes: class 1 mutations constitutively activate the kinase domain and lead to RAS-independent signaling, class 2 mutations induce artificial dimerization of BRAF and RAS-independent signaling and class 3 mutations display reduced or abolished kinase function and require upstream signals. Despite the importance of BRAF mutations in cancer, the clinical associations, genetic interactions and therapeutic implications of non-V600 BRAF mutations have not been explored comprehensively yet. In this study, the author analyzed publically available data from the AACR Project GENIE to further understand clinical associations and genetic interactions of oncogenic BRAF mutations. The analyses identified 93 recurrent BRAF mutations, out of which 50 could be assigned to a functional class based on literature review. The author could show that the frequency of BRAF mutations varies across cancer types and subtypes, and that the BRAF mutation classes are unequally distributed across cancer types and subtypes. Using permutation testing-based co-occurrence analyses, the author defined the genetic interactions of BRAF mutations in multiple cancer types and revealed unexplored genetic interactions that might define clinically relevant subgroups. With non-small cell lung cancer as example, the author further showed that the genetic interactions are BRAF mutation class-specific. The presented analyses explore the properties of oncogenic BRAF mutations and will help to further delineate the complex role of BRAF in cancer.

Comprehensive analysis of changes in protein acetylation in response to lysine deacetylase inhibitors uncovers inhibitor specificities. Lysine deacetylases inhibitors (KDACIs) are used in basic research, and many are being investigated in clinical trials for treatment of cancer and other diseases. However, their specificities in cells are incompletely characterized. Here we used quantitative mass spectrometry (MS) to obtain acetylation signatures for 19 different KDACIs, covering all 18 human lysine deacetylases. Most KDACIs increased acetylation of a small, specific subset of the acetylome, including sites on histones and other chromatin-associated proteins. Inhibitor treatment combined with genetic deletion showed that the effects of the pan-sirtuin inhibitor nicotinamide are primarily mediated by SIRT1 inhibition. Furthermore, we confirmed that the effects of tubacin and bufexamac on cytoplasmic proteins result from inhibition of HDAC6. Bufexamac also triggered an HDAC6-independent, hypoxia-like response by stabilizing HIF1-α, providing a possible mechanistic explanation of its adverse, pro-inflammatory effects. Our results offer a systems view of KDACI specificities, providing a framework for studying function of acetylation and deacetylases.

Lysine acetylation is a frequently occurring posttranslational modification; however, little is known about the origin and regulation of most sites. Here we used quantitative mass spectrometry to analyze acetylation dynamics and stoichiometry in Saccharomyces cerevisiae . We found that acetylation accumulated in growth‐arrested cells in a manner that depended on acetyl‐CoA generation in distinct subcellular compartments. Mitochondrial acetylation levels correlated with acetyl‐CoA concentration in vivo and acetyl‐CoA acetylated lysine residues nonenzymatically in vitro . We developed a method to estimate acetylation stoichiometry and found that the vast majority of mitochondrial and cytoplasmic acetylation had a very low stoichiometry. However, mitochondrial acetylation occurred at a significantly higher basal level than cytoplasmic acetylation, consistent with the distinct acetylation dynamics and higher acetyl‐CoA concentration in mitochondria. High stoichiometry acetylation occurred mostly on histones, proteins present in histone acetyltransferase and deacetylase complexes, and on transcription factors. These data show that a majority of acetylation occurs at very low levels in exponentially growing yeast and is uniformly affected by exposure to acetyl‐CoA. Synopsis Characterization of the basic properties of acetylation in yeast cells by quantitative proteomics reveals distinct acetylation dynamics in different subcellular compartments and provides the first global analysis of acetylation stoichiometry. Acetylation is globally affected by metabolism and growth arrest. Mitochondrial proteins are acetylated within mitochondria. Most acetylation occurs at very low stoichiometry. High stoichiometry acetylation occurs on nuclear proteins. Graphical Abstract Characterization of the basic properties of acetylation in yeast cells by quantitative proteomics reveals distinct acetylation dynamics in different subcellular compartments and provides the first global analysis of acetylation stoichiometry.

Societal upheaval occurred across Eurasia in the sixth and seventh centuries. Tree-ring reconstructions suggest a period of pronounced cooling during this time associated with several volcanic eruptions. Climatic changes during the first half of the Common Era have been suggested to play a role in societal reorganizations in Europe 1 , 2 and Asia 3 , 4 . In particular, the sixth century coincides with rising and falling civilizations 1 , 2 , 3 , 4 , 5 , 6 , pandemics 7 , 8 , human migration and political turmoil 8 , 9 , 10 , 11 , 12 , 13 . Our understanding of the magnitude and spatial extent as well as the possible causes and concurrences of climate change during this period is, however, still limited. Here we use tree-ring chronologies from the Russian Altai and European Alps to reconstruct summer temperatures over the past two millennia. We find an unprecedented, long-lasting and spatially synchronized cooling following a cluster of large volcanic eruptions in 536, 540 and 547  AD (ref.  14 ), which was probably sustained by ocean and sea-ice feedbacks 15 , 16 , as well as a solar minimum 17 . We thus identify the interval from 536 to about 660  AD as the Late Antique Little Ice Age. Spanning most of the Northern Hemisphere, we suggest that this cold phase be considered as an additional environmental factor contributing to the establishment of the Justinian plague 7 , 8 , transformation of the eastern Roman Empire and collapse of the Sasanian Empire 1 , 2 , 5 , movements out of the Asian steppe and Arabian Peninsula 8 , 11 , 12 , spread of Slavic-speaking peoples 9 , 10 and political upheavals in China 13 .

Modern, electrically operated heat pumps are characterized by a high degree of efficiency and represent an attractive alternative to conventional heating systems. However, the noise emissions from heat pumps installed outside can lead to increasing noise pollution in densely populated residential areas, which represents an obstacle to widespread use. As part of a research project, a heat pump mock-up was built based on an outdoor unit in the Fraunhofer IBP. With this mock-up, investigations have now been carried out with a prototypical silencer–resonator concept. The aim was to reduce the sound power on the outlet side of the heat pump mock-up. To estimate the effect of this silencer–resonator concept for heat pumps, FEM simulations were first carried out using COMSOL Multiphysics® with a simplified model. The simulation results validated the silencer–resonator concept for heat pumps and indicated the considerable potential for sound reduction. A measurement was then set up, with which different silencer lengths and absorber thicknesses in the silencer were tested. The measured sound attenuation was higher than the simulated values. The results showed that porous absorbers with sufficient thickness can achieve effective performance in the mid-frequency range. A maximum sound power reduction of 5.7 dB was achieved with the 0.15 m absorber. Additionally, Helmholtz resonators were implemented to attenuate the low-frequency range and tonal peaks. With these resonators sound attenuation was increased to 7.7 dB.